PROKARYOTES
crossm Draft Genome Sequence of Chloracidobacterium sp. CP2_5A, a Phototrophic Member of the Phylum Acidobacteria Recovered from a Japanese Hot Spring Lewis M. Ward,a Shawn E. McGlynn,b Woodward W. Fischera Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USAa; Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ko, Japanb
ABSTRACT The phylum Acidobacteria contains a single known phototrophic member, Chloracidobacterium thermophilum, which was recovered from a hot spring metagenome from Yellowstone National Park. Here, we expand the diversity of the genus Chloracidobacterium with a genome recovered from a hot spring in Japan, extending the known range of this lineage to a new continent.
T
he phylum Acidobacteria comprises widespread but enigmatic bacteria; many subdivisions have been observed in environmental sequencing data, but only a few cultured or well-characterized representatives exist (1). The only known phototroph in this phylum, Chloracidobacterium thermophilum, was originally recovered from metagenomic data from a Yellowstone National Park hot spring (2) and was recently isolated (3). Here, we report the draft genome of Chloracidobacterium sp. strain CP2_5A, recovered from a metagenome of a Japanese hot spring. The metagenome from which this genome was recovered was described in detail by Ward (4). In brief, CP2_5A was recovered from a cone-forming microbial mat from a moderately sulfidic, alkaline hot spring at Nakabusa Onsen in Nagano prefecture, Japan. At the time of sampling, the temperature at the collection site was 32°C with a pH measurement of 8.3. Cells were lysed and DNA was preserved in the field using Zymo Terralyzer BashingBead Matrix and Xpedition Lysis Buffer. DNA was extracted and purified with a Zymo Soil/Fecal DNA extraction kit (Zymo Research, Irvine, CA, USA) and quantified with a Qubit version 3.0 fluorimeter (Life Technologies, Inc., Carlsbad, CA, USA). Purified DNA was submitted to SeqMatic LLC (Fremont, CA, USA) for library preparation and sequencing via Illumina HiSeq technology. Raw sequences were assembled with MegaHit version 1.02 (5) and binned using MetaWatt version 3.5.2 (6). The genome was uploaded to RAST (7) for overall characterization and was assessed for completeness and contamination using CheckM (8). The CP2_5A genome bin is estimated to be 92% complete as determined by CheckM. The genome is 3.41 Mb, with a GC content of 64.2%, and comprises 385 contigs containing 3,023 coding sequences and 52 RNAs. The 16S gene recovered from CP2_5A is 98% identical to that of C. thermophilum strain E. The CP2_5A genome contains a complete suite of genes for anoxygenic phototrophy, including a type 1 reaction center (RCI) and a largely complete bacteriochlorophyll synthesis pathway (only bchM was not recovered in the genome bin). Consistent with the photoheterotrophic lifestyle of the isolated C. thermophilum strain, CP2_5A does not encode carbon fixation pathways. The CP2_5A genome encodes two bc complexes, an alternative complex III, a low-O2-affinity A-family heme-copper oxidoreductase, and a bdVolume 5 Issue 40 e00821-17
Received 3 July 2017 Accepted 18 August 2017 Published 5 October 2017 Citation Ward LM, McGlynn SE, Fischer WW. 2017. Draft genome sequence of Chloracidobacterium sp. CP2_5A, a phototrophic member of the phylum Acidobacteria recovered from a Japanese hot spring. Genome Announc 5:e00821-17. https:// doi.org/10.1128/genomeA.00821-17. Copyright © 2017 Ward et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Lewis M. Ward, [email protected].
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Ward et al.
cytochrome c. The RCI of CP2_5A is similar to that of the Chloracidobacterium isolate: it branches basal to those of phototrophic Chlorobi spp. but more derived than the simple RCIs found in Heliobacteria spp. While one of the bc complexes in CP2_5A clusters with that of C. thermophilum strain E, the other is instead closely related to that from the recently discovered phototrophic phylum Gemmatimonadetes (9), potentially marking horizontal gene transfer between these two clades. The degree of genomic and metabolic similarity between Chloracidobacterium strains found in hot springs across at least two continents suggests a broadly conserved ecology between microbial lineages in similar geochemical environments across large spatial scales. Accession number(s). This whole-genome shotgun project was deposited in DDBJ/ EMBL/GenBank under the accession number NKPT00000000. ACKNOWLEDGMENTS L.M.W. acknowledges support from NASA NESSF (grant NNX16AP39H), NSF (grant OISE 1639454), NSF GROW (grant DGE 1144469), the Lewis and Clark Fund for Exploration and Field Research in Astrobiology, and the ELSI Origins Network. S.E.M. acknowledges support from a MEXT KAKENHI grant-in-aid for challenging exploratory research (grant award 15K14608). W.W.F. acknowledges the support of NASA Exobiology award NNX16AJ57G, the David and Lucile Packard Foundation, and a Stanford University Blaustein Fellowship. We thank Katsumi Matsura and the Environmental Microbiology Laboratory at Tokyo Metropolitan University for laboratory support.
REFERENCES 1. Stamps BW, Corsetti FA, Spear JR, Stevenson BS. 2014. Draft genome of a novel Chlorobi member assembled by tetranucleotide binning of a hot spring metagenome. Genome Announc 2(5):e00897-14. https://doi.org/ 10.1128/genomeA.00897-14. 2. Bryant DA, Costas AMG, Maresca JA, Chew AGM, Klatt CG, Bateson MM, Tallon LJ, Hostetler J, Nelson WC, Heidelberg JF, Ward DM. 2007. Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic acidobacterium. Science 317:523–526. https://doi.org/10.1126/science .1143236. 3. Tank M, Bryant DA. 2015. Chloracidobacterium thermophilum gen. nov., sp. nov.: an anoxygenic microaerophilic chlorophotoheterotrophic acidobacterium. Int J Syst Evol Microbiol 65:1426 –1430. https://doi.org/10.1099/ ijs.0.000113. 4. Ward LM. 2017. Microbial evolution and the rise of oxygen: the roles of contingency and context in shaping the biosphere through time. Ph.D. dissertation, California Institute of Technology, Pasadena, CA. https://doi .org/10.7907/Z9BZ642S. 5. Li D, Luo R, Liu CM, Leung CM, Ting HF, Sadakane K, Yamashita H, Lam TW. 2016. MEGAHIT v1.0: a fast and scalable metagenome assembler driven
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by advanced methodologies and community practices. Methods 102: 3–11. https://doi.org/10.1016/j.ymeth.2016.02.020. Strous M, Kraft B, Bisdorf R, Tegetmeyer HE. 2012. The binning of metagenomic contigs for microbial physiology of mixed cultures. Front Microbiol 3:410. https://doi.org/10.3389/fmicb.2012.00410. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, Mcneil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. https://doi.org/10.1101/gr.186072.114. Zeng Y, Feng F, Medová H, Dean J, Koblížek M. 2014. Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes. Proc Natl Acad Sci U S A 111:7795–7800. https://doi.org/ 10.1073/pnas.1400295111.
genomea.asm.org 2
crossm Draft Genome Sequence of Chloracidobacterium sp. CP2_5A, a Phototrophic Member of the Phylum Acidobacteria Recovered from a Japanese Hot Spring Lewis M. Ward,a Shawn E. McGlynn,b Woodward W. Fischera Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USAa; Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ko, Japanb
ABSTRACT The phylum Acidobacteria contains a single known phototrophic member, Chloracidobacterium thermophilum, which was recovered from a hot spring metagenome from Yellowstone National Park. Here, we expand the diversity of the genus Chloracidobacterium with a genome recovered from a hot spring in Japan, extending the known range of this lineage to a new continent.
T
he phylum Acidobacteria comprises widespread but enigmatic bacteria; many subdivisions have been observed in environmental sequencing data, but only a few cultured or well-characterized representatives exist (1). The only known phototroph in this phylum, Chloracidobacterium thermophilum, was originally recovered from metagenomic data from a Yellowstone National Park hot spring (2) and was recently isolated (3). Here, we report the draft genome of Chloracidobacterium sp. strain CP2_5A, recovered from a metagenome of a Japanese hot spring. The metagenome from which this genome was recovered was described in detail by Ward (4). In brief, CP2_5A was recovered from a cone-forming microbial mat from a moderately sulfidic, alkaline hot spring at Nakabusa Onsen in Nagano prefecture, Japan. At the time of sampling, the temperature at the collection site was 32°C with a pH measurement of 8.3. Cells were lysed and DNA was preserved in the field using Zymo Terralyzer BashingBead Matrix and Xpedition Lysis Buffer. DNA was extracted and purified with a Zymo Soil/Fecal DNA extraction kit (Zymo Research, Irvine, CA, USA) and quantified with a Qubit version 3.0 fluorimeter (Life Technologies, Inc., Carlsbad, CA, USA). Purified DNA was submitted to SeqMatic LLC (Fremont, CA, USA) for library preparation and sequencing via Illumina HiSeq technology. Raw sequences were assembled with MegaHit version 1.02 (5) and binned using MetaWatt version 3.5.2 (6). The genome was uploaded to RAST (7) for overall characterization and was assessed for completeness and contamination using CheckM (8). The CP2_5A genome bin is estimated to be 92% complete as determined by CheckM. The genome is 3.41 Mb, with a GC content of 64.2%, and comprises 385 contigs containing 3,023 coding sequences and 52 RNAs. The 16S gene recovered from CP2_5A is 98% identical to that of C. thermophilum strain E. The CP2_5A genome contains a complete suite of genes for anoxygenic phototrophy, including a type 1 reaction center (RCI) and a largely complete bacteriochlorophyll synthesis pathway (only bchM was not recovered in the genome bin). Consistent with the photoheterotrophic lifestyle of the isolated C. thermophilum strain, CP2_5A does not encode carbon fixation pathways. The CP2_5A genome encodes two bc complexes, an alternative complex III, a low-O2-affinity A-family heme-copper oxidoreductase, and a bdVolume 5 Issue 40 e00821-17
Received 3 July 2017 Accepted 18 August 2017 Published 5 October 2017 Citation Ward LM, McGlynn SE, Fischer WW. 2017. Draft genome sequence of Chloracidobacterium sp. CP2_5A, a phototrophic member of the phylum Acidobacteria recovered from a Japanese hot spring. Genome Announc 5:e00821-17. https:// doi.org/10.1128/genomeA.00821-17. Copyright © 2017 Ward et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Lewis M. Ward, [email protected].
genomea.asm.org 1
Ward et al.
cytochrome c. The RCI of CP2_5A is similar to that of the Chloracidobacterium isolate: it branches basal to those of phototrophic Chlorobi spp. but more derived than the simple RCIs found in Heliobacteria spp. While one of the bc complexes in CP2_5A clusters with that of C. thermophilum strain E, the other is instead closely related to that from the recently discovered phototrophic phylum Gemmatimonadetes (9), potentially marking horizontal gene transfer between these two clades. The degree of genomic and metabolic similarity between Chloracidobacterium strains found in hot springs across at least two continents suggests a broadly conserved ecology between microbial lineages in similar geochemical environments across large spatial scales. Accession number(s). This whole-genome shotgun project was deposited in DDBJ/ EMBL/GenBank under the accession number NKPT00000000. ACKNOWLEDGMENTS L.M.W. acknowledges support from NASA NESSF (grant NNX16AP39H), NSF (grant OISE 1639454), NSF GROW (grant DGE 1144469), the Lewis and Clark Fund for Exploration and Field Research in Astrobiology, and the ELSI Origins Network. S.E.M. acknowledges support from a MEXT KAKENHI grant-in-aid for challenging exploratory research (grant award 15K14608). W.W.F. acknowledges the support of NASA Exobiology award NNX16AJ57G, the David and Lucile Packard Foundation, and a Stanford University Blaustein Fellowship. We thank Katsumi Matsura and the Environmental Microbiology Laboratory at Tokyo Metropolitan University for laboratory support.
REFERENCES 1. Stamps BW, Corsetti FA, Spear JR, Stevenson BS. 2014. Draft genome of a novel Chlorobi member assembled by tetranucleotide binning of a hot spring metagenome. Genome Announc 2(5):e00897-14. https://doi.org/ 10.1128/genomeA.00897-14. 2. Bryant DA, Costas AMG, Maresca JA, Chew AGM, Klatt CG, Bateson MM, Tallon LJ, Hostetler J, Nelson WC, Heidelberg JF, Ward DM. 2007. Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic acidobacterium. Science 317:523–526. https://doi.org/10.1126/science .1143236. 3. Tank M, Bryant DA. 2015. Chloracidobacterium thermophilum gen. nov., sp. nov.: an anoxygenic microaerophilic chlorophotoheterotrophic acidobacterium. Int J Syst Evol Microbiol 65:1426 –1430. https://doi.org/10.1099/ ijs.0.000113. 4. Ward LM. 2017. Microbial evolution and the rise of oxygen: the roles of contingency and context in shaping the biosphere through time. Ph.D. dissertation, California Institute of Technology, Pasadena, CA. https://doi .org/10.7907/Z9BZ642S. 5. Li D, Luo R, Liu CM, Leung CM, Ting HF, Sadakane K, Yamashita H, Lam TW. 2016. MEGAHIT v1.0: a fast and scalable metagenome assembler driven
Volume 5 Issue 40 e00821-17
6.
7.
8.
9.
by advanced methodologies and community practices. Methods 102: 3–11. https://doi.org/10.1016/j.ymeth.2016.02.020. Strous M, Kraft B, Bisdorf R, Tegetmeyer HE. 2012. The binning of metagenomic contigs for microbial physiology of mixed cultures. Front Microbiol 3:410. https://doi.org/10.3389/fmicb.2012.00410. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, Mcneil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. https://doi.org/10.1101/gr.186072.114. Zeng Y, Feng F, Medová H, Dean J, Koblížek M. 2014. Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes. Proc Natl Acad Sci U S A 111:7795–7800. https://doi.org/ 10.1073/pnas.1400295111.
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